CoolMolecules: A Molecular Structure Explorer Robert M. Hanson, Melanie Casavant, Michael McGuan.

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Presentation transcript:

CoolMolecules: A Molecular Structure Explorer Robert M. Hanson, Melanie Casavant, Michael McGuan

Goals of Presentation Basic background: “data driven” chemistry Origin of the website project Goals of the project The site creation process Project outcome Future directions

Basic Background

St. Olaf College Chemistry 123 Dr. Hanson’s Molecular Origami text

observe numerical data turn numerical data into a 3D shape make a hypothesis to explain the shapes (VSEPR theory) test VSEPR theory (predict the shape of more molecules) check predictions with experimental data

Origin of the Website Project

BCCE 17 (two years ago) Molecular Origami + Experimental Data Website (Dr. Bob Hanson) (Dr. Scot Wherland)

Goals of the Project

Complete the database Include biologically relevant molecules Create a widely available, useful interface for the experimental data Make database useful in a classroom setting

The Creation Process

Research New data: A U of M field trip Cambridge Structural Database Interface: Switching to Jmol

Displaying Molecules in 3D Chime: Browser plug-in: must be installed Reads data from file Cannot display vibrating molecules No longer being developed Ugly colors

An Alternative to Chime Jmol: Java applet: runs on all computers with Java enabled Generates a rotatable 3D structure from user input Actively being developed Open source

Incorporating Vibration: Text Books Jmol development team Educational Applications: J-CHEMED list serve High Schools in the area A trip to Carleton 18 th BCCE in Ames, Iowa Text Books

Stages of Development Designing an “Interactive Periodic Table” Searching by various criteria Development of abbreviated databases Incorporating vibration modes Adding new molecules Developing suggested classroom activities

Project Outcome

962 structures (more than 2x as many as we began with) Vibrational modes Dropped the biological molecules for the time being

5 versions of the database (entry level, expanded valence, metals, aromatic complexes, full database) Searchable by atoms, bond type and length, shape and text 20 suggested classroom activities

Drum Roll Please….

Future Directions

Open source project Biologically oriented database Editing the suggested activities Publication in the Journal of Chemical Education

Acknowledgements Miguel Howard (head of jmol development team) The teachers that have given us feedback Dr. Hanson (for staying up in the wee hours of the morning to do the programming I would never want to do myself) All the little people in my life that have helped me come so far

THE END